Magnesium in PDB 3abl: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset):
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset), PDB code: 3abl was solved by H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.137, 207.514, 178.173, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) (pdb code 3abl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset), PDB code: 3abl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg518 b:21.3 occ:1.00 NE2 A:HIS368 2.1 24.8 1.0 OE1 B:GLU198 2.1 29.2 1.0 O B:HOH2033 2.1 19.2 1.0 O B:HOH2031 2.1 21.9 1.0 OD1 A:ASP369 2.2 20.3 1.0 O B:HOH2032 2.2 18.0 1.0 CD2 A:HIS368 3.0 25.8 1.0 CE1 A:HIS368 3.0 28.8 1.0 CD B:GLU198 3.2 26.6 1.0 CG A:ASP369 3.3 21.4 1.0 OE2 B:GLU198 3.5 24.6 1.0 O B:SER197 3.8 22.6 1.0 O A:HOH2035 4.0 17.2 1.0 CB A:ASP369 4.1 21.3 1.0 ND1 A:HIS368 4.1 22.9 1.0 OD1 B:ASP173 4.2 23.5 1.0 CG A:HIS368 4.2 24.5 1.0 O A:HOH2038 4.2 22.0 1.0 OD2 A:ASP369 4.3 18.8 1.0 OD2 B:ASP173 4.3 23.1 1.0 OG1 A:THR294 4.4 22.4 1.0 O A:HOH2023 4.4 21.9 1.0 CG B:GLU198 4.6 17.8 1.0 O A:HOH2020 4.6 22.8 1.0 O A:HOH2010 4.6 17.0 1.0 CG B:ASP173 4.6 27.7 1.0 CB B:GLU198 4.7 19.9 1.0

Magnesium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (15-S X-Ray Exposure Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg1518 b:29.5 occ:1.00 O O:HOH3033 2.0 29.5 1.0 NE2 N:HIS368 2.1 28.1 1.0 OE1 O:GLU198 2.1 30.4 1.0 OD1 N:ASP369 2.2 28.8 1.0 O O:HOH3031 2.2 25.3 1.0 O O:HOH3032 2.2 30.0 1.0 CD2 N:HIS368 3.0 28.4 1.0 CE1 N:HIS368 3.1 30.8 1.0 CD O:GLU198 3.2 32.8 1.0 CG N:ASP369 3.3 30.5 1.0 OE2 O:GLU198 3.6 29.3 1.0 O O:SER197 3.8 28.6 1.0 CB N:ASP369 3.8 32.2 1.0 O N:HOH3035 3.9 25.2 1.0 CG N:HIS368 4.2 28.4 1.0 ND1 N:HIS368 4.2 29.6 1.0 OD2 O:ASP173 4.3 39.1 1.0 OD2 N:ASP369 4.3 30.2 1.0 OG1 N:THR294 4.3 32.4 1.0 OD1 O:ASP173 4.3 28.5 1.0 O N:HOH3038 4.5 26.5 1.0 CG O:GLU198 4.5 27.6 1.0 O N:HOH3023 4.5 27.7 1.0 O N:HOH3010 4.6 28.4 1.0 O N:HOH3020 4.7 30.7 1.0 CG O:ASP173 4.7 33.7 1.0 CB O:GLU198 4.7 24.3 1.0 CA N:ASP369 4.9 29.5 1.0 C O:SER197 4.9 30.1 1.0 N N:ASP369 5.0 29.4 1.0

H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa. A Peroxide Bridge Between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump Proc.Natl.Acad.Sci.Usa V. 106 2165 2009.
ISSN: ISSN 0027-8424
PubMed: 19164527
DOI: 10.1073/PNAS.0806391106